Biosystems最新文献

{"title":"On the transitional character and regularity of planetary abiogenesis","authors":"Serge Dolgikh","doi":"10.1016/j.biosystems.2025.105660","DOIUrl":"10.1016/j.biosystems.2025.105660","url":null,"abstract":"<div><div>The emergence of biology from planetary chemistry remains one of the central open questions in planetary physics, chemistry and biochemistry. In this study, we address an important aspect of this problem: whether abiogenesis is a statistically regular process under broadly defined planetary conditions, or a unique, highly contingent event. To examine it, we introduce a conceptual framework of regularity-relevant classes of adaptive planetary physico-chemical systems: the adaptability ladder model, that formalizes the progression from chemically rich but unorganized environments to stable biochemical systems. The model provides a structured approach to the regularity question, examining potential constrains and bottlenecks in specific adaptive classes and formulate formal statements of the regularity hypothesis: specialized for individual classes and strong (or general) across the full adaptive spectrum. We then assess their differential detectability across observation channels: laboratory simulation, in situ exploration, and remote sensing. Our analysis reveals a strong complementarity between detection channels and the regularity classes, with fragile proto-biotic states accessible primarily through laboratory studies. We observe that under the regularity hypothesis, such early adaptive states should emerge reproducibly under appropriate simulated planetary conditions. This result establishes a direct and testable link between laboratory experimentation and the general question of the regularity of biological emergence, positioning lab-based studies as central to future progress. The framework extends conventional definitions of planetary habitability, traditionally focused on terrestrial-class physical and chemical conditions by incorporating informational aspects, specifically compositional and interactive diversity. This broader perspective informs the strategic prioritization of empirical search efforts, bridging theoretical insights with observable planetary conditions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105660"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward a unified theory of ATP synthesis/hydrolysis: Integrating physics, chemistry, and biology","authors":"Victor Wray,&nbsp;Carey Witkov,&nbsp;Bjarne Andresen","doi":"10.1016/j.biosystems.2025.105680","DOIUrl":"10.1016/j.biosystems.2025.105680","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105680"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145764535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"150 Years since the birth of Lev Berg: Nomogenesis is more relevant today than ever","authors":"A.V. Melkikh","doi":"10.1016/j.biosystems.2025.105670","DOIUrl":"10.1016/j.biosystems.2025.105670","url":null,"abstract":"<div><div>This article is dedicated to the 150th anniversary of the evolutionist Lev Berg and explores his evolutionary ideas. Concepts such as convergence, parallelism, and mimicry are examined. A substantial body of modern research supports Berg's view of evolution as a directional process. In particular, Berg's conclusion that such complex living structures could not have arisen by chance is fully supported by modern calculations. Contemporary examples of parallelism research among animals (including domesticated ones) are considered. Contemporary examples of mimicry research are also considered. The extensive parallelism of species, organs, tissues, etc., also strongly supports Berg's theory. One of Berg's most important ideas was the improbability of random evolution in living systems. The lack of a solution to this problem is one of the main shortcomings of Darwinism. Modern genomic research allows us to further tighten the requirements for this probability, making it negligible.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105670"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145696509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neural plasticity, heterochrony, and the onto-phylogeny of consciousness","authors":"Giuseppe Iurato","doi":"10.1016/j.biosystems.2025.105661","DOIUrl":"10.1016/j.biosystems.2025.105661","url":null,"abstract":"<div><div>From a biological standpoint, the consciousness of a living organism equipped with a complex nervous system may be considered the result of the complex structure and functioning of its brain. Subsequently, the neurobiological bases of consciousness should be traced back to the systemic nature of the macroscale neural circuitries of the brain, which are, in turn, the basic outcomes of certain fundamental microscale neuronal processes whose spatiotemporal action gives rise to a much more complex systemic process called neural plasticity. It is closely related to brain evolution from both phylogenetic and ontogenetic perspectives. It is the primary neurobiological process that links the brain with internal and external environments and the related experiences. Since consciousness is a theoretical construct introduced mainly to account for the (ontogenetically evolving) integrative subject-object intermediation, it might be possible hypothesize the existence of a relationship between consciousness and neural plasticity, at least from a biological standpoint. In these terms, the phylogenetic development of human consciousness, when human lineage started after the split from that of nonhuman primates, might be partially inferred by comparing the (ontogenetic) development of human and nonhuman primate brains, using an extended meaning of the concept of neural plasticity as the main neurobiological process of reference. What seems to emerge from this comparison is the evolutionary occurrence, during anthropogenesis, of distinguishing (transcriptional) heterochronic phenomena concerning neurodevelopmental processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105661"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145642315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Natural history of the transition between RNA to DNA in the early stages of life","authors":"Sávio Torres de Farias ,&nbsp;Marco José","doi":"10.1016/j.biosystems.2025.105671","DOIUrl":"10.1016/j.biosystems.2025.105671","url":null,"abstract":"<div><div>In this work we examine different hypotheses for the fixation of DNA as the principal informational molecule. The emergence of protein RNA-dependent RNA polymerases heralded the beginning of a process that ultimately culminated in the transition from RNA to DNA as the primary informational molecule. To understand this pivotal transition, it is necessary to examine the evolutionary history of nucleic acid polymerases, with particular emphasis on RNA-dependent RNA polymerases, RNA-dependent DNA polymerases, and DNA-dependent DNA polymerases. Instead of resolving the debates over single versus multiple origins of DNA, we adhere to the need to conceptualize early evolution as a dynamic network, driven by horizontal transfer, molecular innovation, and symbiosis between cells and viruses.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105671"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145684326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From nullomers to abundant motifs: Fractals, CpG Bias, and Chargaff’s rules in genomic sequences","authors":"Iván Marqués-Campillo ,&nbsp;Claudia Arbeitman ,&nbsp;Diego Luis González ,&nbsp;Oreste Piro","doi":"10.1016/j.biosystems.2025.105635","DOIUrl":"10.1016/j.biosystems.2025.105635","url":null,"abstract":"<div><div>Nullomers — sequences entirely absent from a given genome — exhibit unexpected fractal structures when visualized using Chaos Game Representation (CGR). Unlike nullomers, rare sequences are defined as those that occur infrequently within the genome. Both nullomers and rare sequences conform to Generalised Chargaff’s Second Parity rule at rates that far exceed random expectations. Beginning with nullomer analysis in <em>Homo sapiens</em>, we identified similar fractal patterns among rare sequences with low genomic frequency. We observe a continuous transition in various organisational properties, such as fractal geometry, CpG content, and Hamming distance between consensus sequences as a function of sequence frequency. In addition, our results reveal a fine-grained interpretation of Chargaff’s rule: sequences exhibit frequency-dependent distributional characteristics. Rare sequences, in particular, display distinctive structural order that differentiates them from more abundant sequences, offering new insights into the underlying architecture of the genome as well as its informational structure. Moreover, these architectural and structural distinctions reinforce the perspective that information and meaning are encoded and managed independently within the genomic language.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105635"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145521270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Obesity, body heat loss, and efficiency in movement","authors":"Adrian Bejan","doi":"10.1016/j.biosystems.2025.105673","DOIUrl":"10.1016/j.biosystems.2025.105673","url":null,"abstract":"<div><div>This article makes an unexpected, counterintuitive theoretical step. Excessive inactive body mass (fat, carried load) has a negative impact on the efficiency of life movement to distances. Also negative is the impact of loss of body heat to the cold ambient. Surprisingly, the two negative impacts evolve naturally to a tradeoff such that the living body benefits from maximal efficiency in movement and access on the globe. The tradeoff reveals the amount of inactive mass (e.g., thickness of fat layer) most beneficial for movement. Tradeoffs between negative impacts govern the evolution (the morphing) of all moving <em>design</em> (animal, vehicle, river, etc.). For example, fat tends to be stored primarily at the interface between the warm inner body and the cold ambient. That's design in nature, configuration evolution. Furthermore, the perception of cold is physical and measurable in terms of physical outcomes: design for greater efficiency in movement on the globe, greater power, easier access, farther reach, economy and longer lifespan. Traditionally, perceptions are thought of as intangibles, opinions, beyond the predictive reach of physics. The physics underpinnings of perceptions, reaffirmed in this article, are essential to the future of robotics and AI, if such technologies are ever to compete with naked animal thought and action.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105673"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How many and which types of primary cells (domains of life) emerged from LUCA, identified employing different genetic codes","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2025.105636","DOIUrl":"10.1016/j.biosystems.2025.105636","url":null,"abstract":"<div><div>The progenote- &gt; cell transition defines the evolutionary stage of the formation of a domain of life. Indeed, the progenote evolutionary stage cannot be or have a domain of life, because the progenote stage does not, by definition, contain cells, being an evolutionary stage with a genotype-phenotype relationship still in formation. Therefore, the progenote stage is certainly cell-free and therefore cannot be a domain of life, which is instead made up of cells. Consequently, it is at the moment in which a cell emerged from the progenote stage that the first domain of life was defined. In fact, this would be the first appearance of a cell in the history of life, since the progenote stage is cell-free. All of this would define the birth of a domain of life because it would represent the first and precise evolutionary point at which the first cell would be born, after the progenote stage. Furthermore, the progenote- &gt; cell transition is completely reflected in the transition from evolving genetic code to frozen genetic code. That is to say, a genetic code in evolution, i.e. still originating, would precisely reflect the definition of progenote because a code that is still originating should have a genotype-phenotype relationship yet to be defined and would identify, by definition, the stage of the progenote. A frozen genetic code, a fully formed, modern genetic code, would imply the cell stage, that is, the abandonment of the progenote stage. Indeed, nothing more than a modern genetic code might indicate the achievement of the cell stage because a fully developed genetic code would imply modern proteins, which in turn would imply that all the structures of that particular evolutionary stage would certainly belong to a cell stage, precisely because they are structures to be considered, in some sense, complete and definitive. In conclusion, the simple observation of specific variants of the genetic code would provide the opportunity to easily identify the domains of life because a genetic code possessed only by a certain type of organism would witness the transition from evolving genetic code to frozen genetic code and consequently the transition from progenote to cell, and would therefore identify a domain of life. In this way, that is to say, by using some variants of the genetic code, the following domains of life have been identified: Bacteria, Methanogens, and Non-Methanogenic Archaea. Eukaryotes, having the same genetic code as non-methanogenic archaea, would belong to the same domain as the latter. The discussion focuses on these three domains of life and their relationship with the domains of life suggested by other hypotheses, and on properties of the variants of the genetic code used to identify these domains.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105636"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Value saturation: Architecture of subjective necessity","authors":"Joseph J. Trukovich","doi":"10.1016/j.biosystems.2025.105642","DOIUrl":"10.1016/j.biosystems.2025.105642","url":null,"abstract":"<div><div>Consciousness requires explanation for how biological architectures reliably generate it. This paper introduces Value Saturation, advancing an identity claim: phenomenal consciousness IS explicit recursive self-modeling saturated by homeostatic significance under perspectival entrapment. Building on the Reaction to Reflection framework, the theory distinguishes sentience (implicit recursion under survival stakes, Level 2) from subjective consciousness (explicit recursion where self-models become manipulable, Levels 4–5). Three integrated components prove necessary: interoceptive binding, homeostatic saturation, and perspectival entrapment. Testable predictions include developmental progression from birth sentience to subjective consciousness around ages 3–5, awareness-manipulation asymmetry, and clinical dissociations producing aberrant rather than absent phenomenology. Converging evidence from prediction error processing, homeostatic feelings, metacognitive hierarchies, and biological computing's thermodynamic advantages supports these requirements. The framework specifies falsification criteria and transforms consciousness into an empirically tractable investigation of organizational transitions in biological systems under thermodynamic constraints.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105642"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145453840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spectral bounds for Sombor and Sombor energy indices: A graph-theoretic study of neurotransmitter molecular networks","authors":"Nalini Devi K. ,&nbsp;Srinivasa G.","doi":"10.1016/j.biosystems.2025.105620","DOIUrl":"10.1016/j.biosystems.2025.105620","url":null,"abstract":"<div><div>This paper applies the recently introduced Sombor index and its spectral extension, the Sombor energy, to model and analyze the structural complexity of neurotransmitter molecular graphs. Let <span><math><mi>G</mi></math></span> denote a molecular graph whose vertices and edges correspond to atoms and covalent bonds, respectively. For each <span><math><mi>G</mi></math></span>, we compute <span><math><mrow><mi>S</mi><mi>O</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span> and <span><math><mrow><mi>S</mi><mi>O</mi><mi>E</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span>, and derive degree-based, spectral-radius, and Frobenius-norm bounds to quantify molecular irregularity. Unlike traditional indices such as Zagreb or Wiener, Sombor descriptors incorporate both degree heterogeneity and geometric weighting, offering refined sensitivity to branching and aromaticity. Comparative analysis across inhibitory (glycine, GABA) and excitatory or modulatory (dopamine, serotonin, norepinephrine) neurotransmitters reveals that higher Sombor measures correspond to greater structural and functional complexity. These results confirm that Sombor-based descriptors capture biologically interpretable differences in molecular organization. The study thereby extends spectral graph theory to neurochemical systems, providing a quantitative framework for cheminformatics, drug design, and functional classification of neurotransmitters.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105620"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}